ISDA

Deposition Date 2016-07-05

Release Date 2016-08-17

Last Version Date 2024-10-16

Entry Detail

PDB ID:

5KQ5

Keywords:

TRANSFERASE

Title:

AMPK bound to allosteric activator

Biological Source:

Source Organism:

Rattus norvegicus (Taxon ID: 10116)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.41 Å

R-Value Free:

0.25

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 61 2 2

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:5'-AMP-activated protein kinase catalytic subunit alpha-1
Gene (Uniprot):Prkaa1
Chain IDs:A
Chain Length:503
Number of Molecules:1
Biological Source:Rattus norvegicus

UniProt ID:P54645 Pfam ID:PF00069, PF21147, PF16579 EC:2.7.11.1

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:5'-AMP-activated protein kinase subunit beta-1
Gene (Uniprot):Prkab1
Mutagens:S108D
Chain IDs:B
Chain Length:204
Number of Molecules:1
Biological Source:Rattus norvegicus

UniProt ID:P80386 Pfam ID:PF16561, PF04739 EC:2.7.11.31

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:5'-AMP-activated protein kinase subunit gamma-1
Gene (Uniprot):Prkag1
Chain IDs:C
Chain Length:330
Number of Molecules:1
Biological Source:Rattus norvegicus

UniProt ID:P80385 Pfam ID:PF00571 EC:2.7.11.31

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
TPO	A	THR	modified residue

Ligand Molecules

6VT

ADP

AMP

SO4

STU

Primary Citation

Discovery and Preclinical Characterization of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1H-indole-3-carboxylic Acid (PF-06409577), a Direct Activator of Adenosine Monophosphate-activated Protein Kinase (AMPK), for the Potential Treatment of Diabetic Nephropathy.

Cameron, K.O, Kung, D.W, Kalgutkar, A.S, Kurumbail, R.G, Miller, R, Salatto, C.T, Ward, J, Withka, J.M, Bhattacharya, S.K, Boehm, M, Borzilleri, K.A, Brown, J.A, Calabrese, M, Caspers, N.L, Cokorinos, E, Conn, E.L, Dowling, M.S, Edmonds, D.J, Eng, H, Fernando, D.P, Frisbie, R, Hepworth, D, Landro, J, Mao, Y, Rajamohan, F, Reyes, A.R, Rose, C.R, Ryder, T, Shavnya, A, Smith, A.C, Tu, M, Wolford, A.C, Xiao, J.Show

J.Med.Chem. 59 8068 8081 (2016)

PMID: 27490827 DOI: 10.1021/acs.jmedchem.6b00866

Abstact

Adenosine monophosphate-activated protein kinase (AMPK) is a protein kinase involved in maintaining energy homeostasis within cells. On the basis of human genetic association data, AMPK activators were pursued for the treatment of diabetic nephropathy. Identification of an indazole amide high throughput screening (HTS) hit followed by truncation to its minimal pharmacophore provided an indazole acid lead compound. Optimization of the core and aryl appendage improved oral absorption and culminated in the identification of indole acid, PF-06409577 (7). Compound 7 was advanced to first-in-human trials for the treatment of diabetic nephropathy.

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Primary Citation of related structures